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Aliases for ZBED9 Gene

Aliases for ZBED9 Gene

  • Zinc Finger BED-Type Containing 9 2 3 5
  • Transposon-Derived Buster4 Transposase-Like Protein 3 4
  • Zinc Finger BED Domain-Containing Protein 9 3 4
  • Zinc Finger Protein 305 Pseudogene 2 2 3
  • SCAN Domain Containing 3 2 3
  • Zinc Finger Protein 452 2 3
  • ZNF305P2 3 4
  • Buster4 3 4
  • SCAND3 3 4
  • ZNF452 3 4
  • SCAN Domain-Containing Protein 3 3
  • DJ1186N24.3 3
  • KIAA1925 4
  • ZFP38-L 3

External Ids for ZBED9 Gene

Previous HGNC Symbols for ZBED9 Gene

  • ZNF305P2
  • ZNF452
  • SCAND3

Summaries for ZBED9 Gene

GeneCards Summary for ZBED9 Gene

ZBED9 (Zinc Finger BED-Type Containing 9) is a Protein Coding gene. GO annotations related to this gene include nucleic acid binding and protein dimerization activity. An important paralog of this gene is ZSCAN12.

Gene Wiki entry for ZBED9 Gene

No data available for Entrez Gene Summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZBED9 Gene

Genomics for ZBED9 Gene

Regulatory Elements for ZBED9 Gene

Enhancers for ZBED9 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F028634 1.4 FANTOM5 Ensembl ENCODE 6.9 -18.8 -18765 1.6 PKNOX1 SREBF2 ZNF48 ZNF2 ZNF366 SCRT2 ZNF391 ZNF263 SP3 OVOL3 ZNF603P ZKSCAN3 ZKSCAN8 ZKSCAN4 ZSCAN9 ZSCAN23 GPX5 GPX6 OR2E1P COX11P1
GH06F028647 1.1 ENCODE 6.4 -32.5 -32471 1.9 ARNT CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZNF766 CBX5 FOS ZKSCAN8 ZKSCAN3 ZKSCAN4 GPX5 ZBED9 GC06M028666 LINC00533 TRT-CGT3-1
GH06F028673 1.3 Ensembl ENCODE 5.1 -58.1 -58090 1.4 ATF1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 GTF3C2 FOS ZNF263 ZKSCAN3 ZNF603P ZKSCAN4 ZKSCAN8 GPX5 GPX6 ZBED9 GC06M028676 TRA-CGC2-1 PIR43008
GH06F028615 1 ENCODE 6.4 -0.1 -88 0.8 ATF1 ARNT CREB3L1 FEZF1 CBX5 ELK1 GATA2 KDM4B GTF2B NCOA1 ZKSCAN3 ZKSCAN4 ZKSCAN8 GPX6 TRIM27 ZNF603P ZBED9 GC06P028619
GH06F028553 1.3 Ensembl ENCODE 4.6 +62.2 62193 1.6 HDGF ATF1 PKNOX1 CREB3L1 YBX1 YY1 ELK1 GATA2 KLF13 MXD4 ZNF603P ZSCAN23 GPX5 OR2E1P COX11P1 ZBED9 GC06M028544 PIR44110 TRR-TCG5-1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZBED9 on UCSC Golden Path with GeneCards custom track

Genomic Location for ZBED9 Gene

Chromosome:
6
Start:
28,571,338 bp from pter
End:
28,616,212 bp from pter
Size:
44,875 bases
Orientation:
Minus strand

Genomic View for ZBED9 Gene

Genes around ZBED9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZBED9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZBED9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZBED9 Gene

Proteins for ZBED9 Gene

  • Protein details for ZBED9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6R2W3-SCND3_HUMAN
    Recommended name:
    SCAN domain-containing protein 3
    Protein Accession:
    Q6R2W3
    Secondary Accessions:
    • Q2NKL9
    • Q5SRJ3
    • Q8TCN2
    • Q96MV9
    • Q96PW3

    Protein attributes for ZBED9 Gene

    Size:
    1325 amino acids
    Molecular mass:
    151666 Da
    Quaternary structure:
    No Data Available

neXtProt entry for ZBED9 Gene

Post-translational modifications for ZBED9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ZBED9 Gene

Domains & Families for ZBED9 Gene

Suggested Antigen Peptide Sequences for ZBED9 Gene

Graphical View of Domain Structure for InterPro Entry

Q6R2W3

UniProtKB/Swiss-Prot:

SCND3_HUMAN :
  • Contains 1 integrase catalytic domain.
Domain:
  • Contains 1 integrase catalytic domain.
  • Contains 1 SCAN box domain.
genes like me logo Genes that share domains with ZBED9: view

No data available for Gene Families for ZBED9 Gene

Function for ZBED9 Gene

Gene Ontology (GO) - Molecular Function for ZBED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IBA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IBA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with ZBED9: view
genes like me logo Genes that share phenotypes with ZBED9: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for ZBED9 Gene

Localization for ZBED9 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ZBED9 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for ZBED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IBA --
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with ZBED9: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for ZBED9 Gene

Pathways & Interactions for ZBED9 Gene

SuperPathways for ZBED9 Gene

No Data Available

Interacting Proteins for ZBED9 Gene

Gene Ontology (GO) - Biological Process for ZBED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter IEA --
GO:0015074 DNA integration IEA --
genes like me logo Genes that share ontologies with ZBED9: view

No data available for Pathways by source and SIGNOR curated interactions for ZBED9 Gene

Transcripts for ZBED9 Gene

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZBED9 Gene

No ASD Table

Relevant External Links for ZBED9 Gene

GeneLoc Exon Structure for
ZBED9
ECgene alternative splicing isoforms for
ZBED9

Expression for ZBED9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ZBED9 Gene

Protein differential expression in normal tissues from HIPED for ZBED9 Gene

This gene is overexpressed in Lung (45.5) and Placenta (23.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ZBED9 Gene



Protein tissue co-expression partners for ZBED9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZBED9 Gene:

ZBED9
genes like me logo Genes that share expression patterns with ZBED9: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for ZBED9 Gene

Orthologs for ZBED9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ZBED9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCAND3 35 34
  • 99.57 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SCAND3 35 34
  • 86.26 (n)
OneToOne
mouse
(Mus musculus)
Mammalia 2410018M08Rik 35
  • 32 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 32 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101733657 34
  • 51.36 (n)
zebrafish
(Danio rerio)
Actinopterygii BX664605.1 35
  • 34 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 27 (a)
ManyToMany
Species where no ortholog for ZBED9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ZBED9 Gene

ENSEMBL:
Gene Tree for ZBED9 (if available)
TreeFam:
Gene Tree for ZBED9 (if available)

Paralogs for ZBED9 Gene

genes like me logo Genes that share paralogs with ZBED9: view

Variants for ZBED9 Gene

Sequence variations from dbSNP and Humsavar for ZBED9 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs10223644 -- 28,611,195(+) AGTCC(G/T)GGTAT intron-variant
rs10434846 -- 28,611,951(+) accct(A/G)tggac intron-variant
rs10596397 -- 28,617,328(+) TCTAT(-/CTAT)TTATT upstream-variant-2KB
rs10616658 -- 28,588,422(+) GTTTG(-/TT)TTGTT intron-variant, upstream-variant-2KB
rs111598448 -- 28,575,217(+) AATTC(A/G)GTCCA reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for ZBED9 Gene

Variant ID Type Subtype PubMed ID
nsv830621 CNV gain 17160897
nsv601210 CNV gain 21841781
nsv1074388 CNV deletion 25765185
esv3608458 CNV gain 21293372
esv3608457 CNV gain 21293372
esv3576110 CNV gain 25503493
dgv3296n106 CNV deletion 24896259

Variation tolerance for ZBED9 Gene

Residual Variation Intolerance Score: 27.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.90; 59.23% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZBED9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZBED9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZBED9 Gene

Disorders for ZBED9 Gene

Relevant External Links for ZBED9

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ZBED9

No disorders were found for ZBED9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZBED9 Gene

Publications for ZBED9 Gene

  1. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. (PMID: 23533661) Hayward A. … Jern P. (PLoS ONE 2013) 2 3 4 64
  2. On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain. (PMID: 23550032) Llorens C. … Moya A. (Mob Genet Elements 2012) 2 3 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall A.J. … Beck S. (Nature 2003) 3 4 64

Products for ZBED9 Gene

Sources for ZBED9 Gene

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